The Beginning After The End
by Jez0209
Summary: Set after the Season 5 finale. Booth goes after Brennan to Indonesia and they have since become a couple; But what happens next? What will they do when they have to go back to "normal"?
1. Chapter 1

_**I know, I know, it has been like a thousand years since I said that I would post th**__**is, but hey!, in my defense I can't post unless I like how I wrote it, besides, I've been College kinda busy. Anyway, it's finally here for those who still want to read it. Multichapter, hope you enjoy it!**_

_**By the way, I will be writing the name of some songs at the bottom of some chapters, that, because those songs came to my mind when I was writing them.**_

**The Beginning After The End**

Maluku, Indonesia. The clock said seven in the morning and the sun was just coming out. There was a bedroom, dimly illuminated by the sunlight that was filtering through the curtains, and there was a handsome man, sitting on the floor right by that window; his chocolate eyes admiring the beautiful, sleeping form of the woman who was lying face down on the bed. That man was Seeley Booth, and that woman Temperance Brennan.

It had been a year since that day in which Booth had decided that he couldn't let Brennan go; one year since he had come to Indonesia to confess his feelings to her, and one year since she had taken him in her life. Many things had happened since that day; many things had been done and said, and many laws had been broken, mostly the laws of physics; and it had been in those moments in which he had memorize and love every existent curve of her body, that he confirmed that he indeed belong with her and to her.

Remembering those things made Booth smile inwardly; he sighed and stood up reluctantly; she was sleeping so peacefully that he didn't want to disturb her, let alone wake her up, but it was his last day there, their last day together there and he wanted to make the most of it. He walked slowly towards the bed and bent down to get closer to her.

-Bones… -he whispered softly -Bones… -he tried again shaking her slightly –Hey baby, wake up.

-Hmmmmm… -she mumbled and stirred.

-Baby, come on -he said, planting a gentle kiss on her bare shoulder making her finally turn around.

-Hey! Good morning- she said groggily.

-Good morning beautiful.

-Come back to bed – she told him, pulling him down for a kiss.

-You know I would love to –he told her between kisses -in fact there is nothing I would rather do, but I can't.

-Why?

-Because I'm leaving in a few hours.

Brennan stilled, staring at Booth, analyzing his words that were sinking slowly in her.

-I forgot – she said, letting go of Booth and sitting up on the bed –You have to leave before I do.

-That's right –he said –come on, we have a lot of things to do before I leave –he said, standing up, but Brennan remained motionless.

-Why can't we arrive at the same time? – she asked him innocently, her eyes full of confusion.

-Because, there will be people waiting for you at the airport, and if we arrive together they are gonna start asking all these questions, why wasn't I in the Army and stuff like that.

-Is that really that terrible?

-Is not terrible at all –he told her sitting on the bed again- it's just that I don't think that it would be the proper way for our friends to find out about us, they deserve better than that.

-You're right; I don't even know why I asked you that, I blame my drowsiness for it.

-It's okay.

-I don't want you to go yet –she said nonchalantly all of the sudden, taking Booth aback because of her unexpected admission.

-I don't want to leave either, but…

-But you have to; I know that –she said a little annoyed.

-Ok so, let's go –he said standing up again and offering her his hand to help her get up from bed. She took his hand, but pulled him back to bed and he landed on top of her.

-Do you think we have time to have sexual intercourse –she asked him seductively.

-Bones…

-Make love?

-That's much better –he said, and they started to kiss passionately. Booth was just taking his shirt off when his stomach rumbled; he ignored it and tried to focus and what they were doing, but it rumbled again and this time and despite himself, he started to laugh and so did Brennan –How about some breakfast? -he said leaning his head on her shoulder still laughing –As you can see, I may pass out if I don't eat something soon.

-Ok –Brennan said laughing as well –Let me get a shower.

Booth got off from on top of Brennan and she got up grabbing some clothes and walking towards the bathroom.

-Booth –she called him out.

-Yeah?

-Aren't you coming? –she said putting her head out of the door with a mischievous smile on her face.

Booth didn't need to be asked twice, he almost jumped out of the bed, quickly following Brennan inside the bathroom.

The rest of the day they spent it doing all kinds of things but nothing really, the only important thing only being in each others company. The time came, and on all the way to the airport they didn't share a word, Brennan looking through the window's car and Booth looking at Brennan, with her hand in his, never letting go of it. When they entered to the airport they were still holding hands, walking slowly like if they didn't want to reach their destination. Almost getting to the boarding area, Booth stopped abruptly pulling on Brennan's hand and she stopped as well, giving Booth a confused look.

-Are you ok? –He told her, concern in his eyes.

-Yes, why are you asking?

-You seem upset.

-No, I'm just… -she inhaled deeply and looked down to the floor –I'm so used to have you around and now that you are leaving… well… I'm going to miss you… a lot.

Booth placed his right index finger under her chin to lift her face up so he could look at her in the eyes.

-I'm gonna miss you a lot too, probably more than you will miss me–he said, smiling sweetly and making her smile too.

-There is no way you can know who is going to miss who the most.

Booth chuckled and stepped closer to Brennan; he placed a hand on her cheek caressing it gently.

-It's just a week Bones, just a week, and then we'll have all the time in the world.

-I know –she said, her eyes filling with tears and she looked away –I'm sorry, I don't know what's wrong with me.

-No need to apologize baby –He told her and kissed her tenderly, surrounding Brennan's waist with both arms; she put her arms around his neck. After a few seconds they pulled apart in need from air. Booth leaned his forehead against hers.

-I have to go –he whispered sadly.

-Ok

Booth gave her one last short kiss on the lips and then one on the cheek hugging her tightly.

-I'll see you in a week – he whispered against her hair, and Brennan nodded.

They pulled apart from their embrace and he took one of her hands between his.

-I love you –he told her sincerely.

-Booth, I…

-It's okay Bren-he cut her off and she sighed resigned. He grabbed his luggage and took a few steps backwards, not breaking eye contact with Brennan and not really wanting to let go of her hand.

-Call me when you get to Washington –Brennan said, he nodded and turned around starting to walk away. Before giving his ticket away to the flight attendant, Booth turned around and looked at Brennan one last time, she waved goodbye and he did the same before turning his back to her and walking away. Brennan stood there until she couldn't distinguish his silhouette anymore from the crowd.

Neither of them could sleep that night, nor the following four nights, empty cold beds and sweet memories hunting them each and every of those nights.

_Empty Road _by Natalie Walker

**So how was it?**

**Rem****ember, not a native speaker of English.**


	2. Chapter 2

_**Long, long time since I last updated this. I'm a horrible person, I know, but I've already finished College which means that I now have a job, which means that I don't have as much free time as I would like.**_

_**Enjoy!**_

-What do you mean by "escaped"? –Booth said angrily to his phone while pacing around the platform impatiently –Yes, I know what "escape" means, but how did it happen?... no, I…why are you being so damn literal today –he said, his frustration growing.

-Is it just me, or Booth has been a little moody lately? –Angela told Cam in a low voice. Both women had been observing Booth's ranting attentively for a while now.

-Nop, he's moody, - Cam stated - and I think I know the reason.

Angela smiled; of course they both knew the reason of Booth's behavior.

-I just hope she arrives before he shoots someone.- she added, and then flinched at Booth's yelling.

-So get that lazy ass of yours to work and… Oh really? Well, that goes to you too! –Booth shouted to his phone and hang up roughly.

-Is everything alright?- Cam asked cautiously; Booth turned to face her and sighed tiredly, running his fingers through his hair.

-Well, apparently, I have a bunch of idiots working for me that can't manage to keep an eye on a single guy and, as if that wasn't enough, the guy I was on the phone with had some interesting things to say to me.

-I'm sure everything is gonna be fine –Cam told him reassuringly.

-I hope. Have your people identified the girl on the picture? –Booth asked her.

-I'm working on it. –Angela intervened.

-Work faster then. -Booth told her rudely and gave his back to her, ready to leave.

-Excuse me? –Angela said indignantly -Did someone had a bowl of Jerk O's for breakfast this morning?

Booth turned around, abruptly, evidently irritated. Cam shot him a warning gaze before he did anything stupid; that seemed to calm him down a little.

-I'm just saying that if Bones was here, we would have already solved the case. –he said with a softer tone.

-Booth, we are working as fast as we can. –Cam told him while trying to lead him to the stairs.

-Fine, I leave. I have a suspect to interrogate anyway.

-Do you mind if I go with you? -a female voice coming out of nowhere said.

-I rather n…-Booth turned around, and was rendered speechless by the image of Brennan standing in front of him. Cam, Angela and him had been so immerse into their conversation that they didn't notice when Brennan had joined them in the platform. She had been witnessing their little argument ever since.

-Bren!-Angela shouted excitedly making her way to Brennan –Hi sweetie! When did you arrive?

-A few hours ago Ange.

-Dr. Brennan, so nice to have you back –Cam said, taking her turn to hug Brennan; once she did, she –as well as Angela, turned her attentions to Booth, waiting for him to react in some way other than staring at Brennan completely dumbfounded, but since Booth seem inhibited by her and Angela's presence, she moved on to plan B.

-Angela, what was that thing you wanted to show me earlier today? –she asked the artist.

-What? –Angela said, looking at her confused.

-That thing you told me Hodgins discovered. –Cam told her, making special emphasis on the word "thing."

Angela kept looking at Cam clueless, until she finally got the hint.

-Oh! You mean "that." Sorry, I have completely forgotten.

-So let's go then. We'll leave guys alone.

Both women headed to Angela's office, Booth's eyes following their every move. Once they were nowhere to be seen, he got closer to Brennan smiling widely. He kept his distance to keep himself from doing something impulsive, like kissing her.

-What are you doing here? – he told her –I thought you'd arrive in 3 days.

-I was supposed to –she answered smiling back –but… I missed you,- she said, her last words made Booth's face light up –so I hurried things up to be home sooner.

-You should've called me to pick you up at the airport.

-I figure you could be busy.

-I could never be busy for you.- he said charmingly, looking at her straight in the eyes.

-Why are you looking at me like that? –Brennan said, when se noticed the intensity in his eyes.

-Nothing, It's just… I'm glad you're back –he said, smiling sweetly.

-I'm glad I'm back too.

-So… shall we go? –Booth said breaking the spell.

-Sure.

They both made their way to the exit, keeping a safe distance from each other, for they didn't want anyone to have the least suspicion about them. Outside, they got in the SUV. They didn't say anything else to each other; they only exchanged complicity looks and smiles once in a while. The fact of being together again was the only thing that mattered at the moment.

Booth had just driven a few blocks when he suddenly pulled over.

-Why are you pulling over? –Brennan asked, disconcerted.

Booth didn't reply, he simply pulled her close and kissed her fondly.

-Welcome home Bones. –he said, looking at her with utter devotion. Brennan felt shy all of the sudden.

-Thanks Booth. –she replied softly.

**How was it? Is a small one, but next chapters will be better.**


	3. Chapter 3

_**Sorry for the delay. I'll try to update sooner next time, hope you enjoy it!**_

_**Thanks to those who took the time to post a comment.**_

It had been threes weeks since Brennan and Booth had reunited; three weeks in which everything had gone incredibly well between the two of them, just like it had when they were in Indonesia. During those weeks, they had been as discrete as possible, acting like nothing had changed between them for they hadn't told their friends yet about the real nature of their relationship. However, when no one was around, they would act like what they really were, like what Booth had always wanted them to be: a couple.

That particular morning, Booth had woken up alone, surrounded by nothing but darkness and silence. It was when he reached out for the other side of the bed, and found nothing that he remembered he was alone, and that it all was Angela's fault. The night before, just when Brennan and he were getting ready to leave, Angela made a surprise appearance to practically drag Brennan out of her office, claiming that they hadn't had a "lady's night" in a long time. Brennan merely gave Booth a quick, apologetic look, and they agreed with furtive glances to give up their plans for the night; He just stood there, hopeless and upset, watching his lady go. Therefore, that night, he dined and slept alone in his apartment. It was on moments like those that he still briefly wondered, if everything was nothing more than beautiful dream.

Hours later, Booth found himself on his chair, in his office, feeling quite annoyed and frustrated because apparently all crime had decided to take the day off, hence ruining the only opportunity he had to spend some time with Brennan without raising eyebrows or having the need to be careful. He glanced anxiously at the cell phone lying on his desk for the millionth time, bitterly waiting for a call that informed him someone had found a body. He was just thinking about the kind of excuse he could make to explain an unexpected and unnecessary visit to the Jeffersonian when the phone rang. Not that he was happy that someone had been murdered, but he pretty much ran to get out of his office as soon as he hung up the phone.

All his hopes to see Brennan were crushed when he arrived to her office and she wasn't there. He sighed, and dialed the number he knew by heart.

-Brennan.- a female voice on the other line said.

-Bones, where are you?- Booth asked.

-At the crime scene.- she answered blatantly -Where are you?

-In your office.

-What are you still doing there?- she asked, making him feel stupid -We have a case.

-I know we have a case, but I came here to pick you up.

-Oh! I thought we had to arrive separately. –she said, a hint of confusion in her voice.

-Not all the time Bones, besides we always arrive to crime scenes together.

-I'll wait for you next time Booth, I promise.- she said apologetically.

-It's ok Bones. - he assured her. He heard someone in the background calling her name.

-I have to go Booth.- she told him -I'll see you later.

-Ok. I'm on my way baby.- Booth hung up the phone and turned on his heels to leave, only to find himself face to face with Angela who was looking at him questioningly. His eyes widened unwittingly.

-Angela.- Booth uttered, surprise evident in his voice.

-Hey B-man.- she greeted -Who were you talking to?- she asked mischievously.

-Ah… another agent from the FBI.- he lied.

-Really? I didn't know you called each other "baby."

-I would really like to continue this conversation, but Bones is waiting for me in a crime scene, so… -Booth said nervously and walked past her rapidly.

-Booth!- she called out -Booth!- it was of no use for the agent had already left. Angela sighed; she was definitely going to discover who "baby" was.

* * *

-What took you so long?- Brennan asked Booth as soon as she saw him. She looked a little upset.

-I ran into Angela,- he said -Long story.- he added when he noticed Brennan´s confused expression -What do we got?- he asked her, making his way to the dead body.

-Male, Caucasian, mid twenties. I would say he's been dead for about 36 hours judging by the degree of decomposition in the body.- she explained.

-Cause of death?

-Well, the body presents multiple gunshots, but the head is missing.- she informed before an FBI agent approached them. He was holding a visibly drunken man by the arm.

-Agent Booth, we found this man here passed out a few meters away from the crime scene; his hands covered in blood.- he told Booth. The drunken man caught a glimpse of the death body.

-Uh! It wasn't me.- he exclaimed.

-Well, I decide that. Thank you Richards, I'll take care of that.- he told the agent who left, and grabbed the drunken man, turning him to put the handcuffs on.

-Hey! Who's the hottie right here?- he said, referring to Brennan who put a disgusted face. -I would definitely let her handcuff me if you know what I mean.- he implied.

-Watch out buddy, is my girlfriend you are talking about.- Booth warned, tightening the handcuffs.

-Ouch!- the man winced -I didn't know you guys from the FBI were allowed to date other agents.

-She's not an agent, -he answered simply -and is none of your business. Take him to the FBI.- he asked to another agent, and handed the man over.

-I'm perfectly capable of defending myself Booth.- Brennan told him, annoyance in her voice.

-I know Bones, but he was talking to me.

Before Brennan could reply, they stopped dead on their tracks when they turned on the other direction and found Hodgins staring at them in complete awe, a bemused expression on his face reflecting little by little. He was holding the missing head.

-I found the skull,- he muttered -in case someone cares.

* * *

-You know Bones, you could've just told me that Hodgins was here too.- he told her a few minutes later.

-I assumed you'd know. It's only logical for him to be here since we are on a crime scene.- she said simply.

-He doesn't always come. How was I supposed to know that he would come today?

-I don't see what the problem is; he probably didn't even hear you.

-Didn't you see the look on his face? Trust me Bones, he heard me.- he said, visibly worried -You know what? I should just go and find out.- Booth looked around searching for him -There he is; I'll be right back Bones.- he told her and walked towards Hodgins who was analyzing some particles in a device; he seemed very concentrated.

-Listen Hodgins, about what you heard before…

-You are so dating Doctor Brennan,- he interrupted Booth, not taking his eyes off the screen before him. He said it in a way that Booth found incredibly annoying; as annoying as the wide smile he currently had upon his face. Booth felt like choking him.

-I'll kill you if you tell anyone. -he warned, sternly.

-On no, you wouldn't. -Hodgins replied, still smiling.

-Trust me, I would.

-No you wouldn't.- Hodgins said, finally looking at Booth -You wouldn't dare to leave a child fatherless.

-Of course I… wait... what!- Booth exclaimed, Hodgins' smile only grew wider.

-I'm going to be a father. -he informed, happily.

-Wow! Congratulations man. -Booth told him enthusiastically, and hugged him.

-But you cannot tell anybody,- Hodgins said, suddenly serious -Angela would kill me if she finds out I told you.

-I won't tell anyone, but you can't say a thing about what you heard.

-Sounds fair to me.- Hodgins told him, and with that, Booth turned to leave -By the way,- Hodgins said, stopping Booth -Congratulations to you too, it was about time.- Booth simply smiled, and walked away to meet Brennan who was waiting for him.

-What did he say?- Brennan asked, genuine curiosity filling her voice. They were now walking side by side towards the SUV.

-He won't tell anyone.

-That's all?

-Yeah. Hey! What do you say if tonight it's just you and me, and that restaurant you like so much?- Booth offered, attempting to change the subject. Brennan noticed.

-I can´t, Angela wants to have dinner with me.

-Again?

-She says she has to tell me something important.- she said casually -Is that all Hodgins told you? I saw you hugging him; I had never seen you hugging Hodgins.

- This was… a guy thing, that's all. -he said dismissively.

-A guy thing?

-You know, he congratulated me for being with you so I hug him.

-Why would he congratulate you for that?

-He said it was about time, and… never mind.- Brennan gave him a suspicious look.

-Ok.- she agreed and got into the SUV.

Booth knew there was no way he had convinced her, but he wasn't worried; he would have plenty of time to deal with that later, at home. He then remembered Hodgins words _"It was about time," _he couldn't agree more; he had thought the exact same thing more than one year ago. If only Hodgins knew…

Booth smiled knowingly.

**Let me know what you think; it'll be greatly appreciated. **


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